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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2021-05-10, 22:46 based on data in:

        General Statistics

        Showing 384/384 rows and 3/5 columns.
        Sample Name% Dups% GCM Seqs
        jxe.033_R1
        96.7%
        53%
        0.0
        jxe.033_R2
        90.0%
        55%
        0.0
        jxe.034_R1
        97.0%
        53%
        0.1
        jxe.034_R2
        90.6%
        55%
        0.1
        jxe.035_R1
        97.6%
        53%
        0.1
        jxe.035_R2
        91.1%
        55%
        0.1
        jxe.036_R1
        95.9%
        53%
        0.0
        jxe.036_R2
        89.3%
        54%
        0.0
        jxe.037_R1
        96.3%
        54%
        0.1
        jxe.037_R2
        87.6%
        55%
        0.1
        jxe.038_R1
        95.8%
        53%
        0.0
        jxe.038_R2
        87.6%
        55%
        0.0
        jxe.039_R1
        96.2%
        54%
        0.1
        jxe.039_R2
        87.8%
        54%
        0.1
        jxe.040_R1
        96.8%
        54%
        0.1
        jxe.040_R2
        90.9%
        55%
        0.1
        jxe.041_R1
        97.1%
        53%
        0.0
        jxe.041_R2
        90.5%
        54%
        0.0
        jxe.042_R1
        97.1%
        53%
        0.1
        jxe.042_R2
        90.6%
        55%
        0.1
        jxe.043_R1
        96.8%
        53%
        0.0
        jxe.043_R2
        86.9%
        54%
        0.0
        jxe.044_R1
        96.3%
        53%
        0.1
        jxe.044_R2
        88.4%
        54%
        0.1
        jxe.045_R1
        97.4%
        53%
        0.1
        jxe.045_R2
        90.9%
        55%
        0.1
        jxe.046_R1
        96.5%
        53%
        0.1
        jxe.046_R2
        89.7%
        54%
        0.1
        jxe.047_R1
        96.8%
        53%
        0.0
        jxe.047_R2
        90.2%
        54%
        0.0
        jxe.048_R1
        96.4%
        53%
        0.1
        jxe.048_R2
        88.9%
        54%
        0.1
        jxe.049_R1
        97.4%
        53%
        0.1
        jxe.049_R2
        90.2%
        55%
        0.1
        jxe.050_R1
        96.8%
        53%
        0.0
        jxe.050_R2
        90.4%
        54%
        0.0
        jxe.051_R1
        96.9%
        52%
        0.0
        jxe.051_R2
        89.8%
        54%
        0.0
        jxe.052_R1
        95.8%
        53%
        0.0
        jxe.052_R2
        90.3%
        55%
        0.0
        jxe.053_R1
        96.8%
        53%
        0.0
        jxe.053_R2
        89.4%
        55%
        0.0
        jxe.054_R1
        97.0%
        53%
        0.1
        jxe.054_R2
        91.0%
        55%
        0.1
        jxe.055_R1
        95.9%
        54%
        0.0
        jxe.055_R2
        86.2%
        55%
        0.0
        jxe.056_R1
        96.0%
        54%
        0.1
        jxe.056_R2
        89.0%
        55%
        0.1
        jxe.057_R1
        96.3%
        53%
        0.0
        jxe.057_R2
        89.7%
        54%
        0.0
        jxe.058_R1
        96.5%
        53%
        0.1
        jxe.058_R2
        90.9%
        54%
        0.1
        jxe.059_R1
        97.0%
        53%
        0.0
        jxe.059_R2
        89.8%
        55%
        0.0
        jxe.060_R1
        65.0%
        53%
        0.0
        jxe.060_R2
        21.6%
        55%
        0.0
        jxe.061_R1
        97.2%
        53%
        0.1
        jxe.061_R2
        90.2%
        54%
        0.1
        jxe.062_R1
        96.7%
        54%
        0.1
        jxe.062_R2
        90.8%
        54%
        0.1
        jxe.063_R1
        96.4%
        53%
        0.0
        jxe.063_R2
        87.8%
        54%
        0.0
        jxe.064_R1
        96.0%
        54%
        0.1
        jxe.064_R2
        91.3%
        54%
        0.1
        jxe.065_R1
        97.0%
        53%
        0.0
        jxe.065_R2
        91.0%
        54%
        0.0
        jxe.066_R1
        97.3%
        53%
        0.0
        jxe.066_R2
        91.7%
        54%
        0.0
        jxe.067_R1
        96.4%
        53%
        0.0
        jxe.067_R2
        87.5%
        54%
        0.0
        jxe.068_R1
        97.1%
        53%
        0.0
        jxe.068_R2
        91.2%
        54%
        0.0
        jxe.069_R1
        96.7%
        54%
        0.1
        jxe.069_R2
        90.9%
        55%
        0.1
        jxe.070_R1
        97.0%
        53%
        0.1
        jxe.070_R2
        90.8%
        54%
        0.1
        jxe.071_R1
        96.5%
        54%
        0.1
        jxe.071_R2
        88.8%
        54%
        0.1
        jxe.072_R1
        95.8%
        53%
        0.0
        jxe.072_R2
        87.5%
        54%
        0.0
        jxe.073_R1
        97.1%
        53%
        0.0
        jxe.073_R2
        89.0%
        54%
        0.0
        jxe.074_R1
        95.0%
        53%
        0.0
        jxe.074_R2
        86.8%
        54%
        0.0
        jxe.075_R1
        95.7%
        53%
        0.0
        jxe.075_R2
        86.0%
        54%
        0.0
        jxe.076_R1
        95.6%
        53%
        0.0
        jxe.076_R2
        90.6%
        54%
        0.0
        jxe.077_R1
        96.5%
        53%
        0.0
        jxe.077_R2
        89.5%
        54%
        0.0
        jxe.078_R1
        96.2%
        54%
        0.1
        jxe.078_R2
        90.5%
        54%
        0.1
        jxe.079_R1
        96.6%
        53%
        0.0
        jxe.079_R2
        86.4%
        54%
        0.0
        jxe.080_R1
        97.2%
        52%
        0.0
        jxe.080_R2
        91.5%
        54%
        0.0
        jxe.081_R1
        97.6%
        53%
        0.1
        jxe.081_R2
        92.2%
        54%
        0.1
        jxe.082_R1
        98.3%
        53%
        0.1
        jxe.082_R2
        92.7%
        55%
        0.1
        jxe.083_R1
        96.7%
        54%
        0.1
        jxe.083_R2
        90.4%
        54%
        0.1
        jxe.084_R1
        96.6%
        54%
        0.0
        jxe.084_R2
        89.9%
        55%
        0.0
        jxe.085_R1
        96.5%
        53%
        0.1
        jxe.085_R2
        88.8%
        55%
        0.1
        jxe.086_R1
        94.9%
        53%
        0.0
        jxe.086_R2
        86.6%
        54%
        0.0
        jxe.087_R1
        95.4%
        53%
        0.0
        jxe.087_R2
        85.5%
        54%
        0.0
        jxe.088_R1
        96.9%
        53%
        0.1
        jxe.088_R2
        91.1%
        55%
        0.1
        jxe.089_R1
        97.2%
        53%
        0.0
        jxe.089_R2
        90.8%
        54%
        0.0
        jxe.090_R1
        96.9%
        53%
        0.1
        jxe.090_R2
        90.8%
        54%
        0.1
        jxe.091_R1
        96.5%
        53%
        0.0
        jxe.091_R2
        85.2%
        54%
        0.0
        jxe.092_R1
        96.4%
        53%
        0.1
        jxe.092_R2
        89.2%
        54%
        0.1
        jxe.093_R1
        96.7%
        53%
        0.0
        jxe.093_R2
        89.4%
        54%
        0.0
        jxe.094_R1
        97.4%
        53%
        0.1
        jxe.094_R2
        90.7%
        55%
        0.1
        jxe.095_R1
        96.9%
        53%
        0.1
        jxe.095_R2
        88.8%
        54%
        0.1
        jxe.096_R1
        97.0%
        54%
        0.1
        jxe.096_R2
        90.6%
        54%
        0.1
        jxe.097_R1
        98.0%
        52%
        0.1
        jxe.097_R2
        90.5%
        54%
        0.1
        jxe.098_R1
        62.4%
        53%
        0.0
        jxe.098_R2
        13.3%
        55%
        0.0
        jxe.099_R1
        96.3%
        53%
        0.0
        jxe.099_R2
        86.9%
        55%
        0.0
        jxe.100_R1
        96.5%
        54%
        0.1
        jxe.100_R2
        91.9%
        55%
        0.1
        jxe.101_R1
        96.7%
        54%
        0.1
        jxe.101_R2
        91.0%
        54%
        0.1
        jxe.102_R1
        96.5%
        54%
        0.1
        jxe.102_R2
        90.8%
        54%
        0.1
        jxe.103_R1
        95.8%
        54%
        0.1
        jxe.103_R2
        85.3%
        55%
        0.1
        jxe.104_R1
        96.4%
        54%
        0.1
        jxe.104_R2
        89.3%
        55%
        0.1
        jxe.105_R1
        97.0%
        53%
        0.1
        jxe.105_R2
        90.9%
        54%
        0.1
        jxe.106_R1
        97.1%
        53%
        0.1
        jxe.106_R2
        90.8%
        55%
        0.1
        jxe.107_R1
        96.6%
        54%
        0.1
        jxe.107_R2
        90.6%
        54%
        0.1
        jxe.108_R1
        63.4%
        53%
        0.0
        jxe.108_R2
        17.0%
        54%
        0.0
        jxe.109_R1
        96.4%
        54%
        0.0
        jxe.109_R2
        88.8%
        55%
        0.0
        jxe.110_R1
        94.8%
        54%
        0.0
        jxe.110_R2
        86.8%
        54%
        0.0
        jxe.111_R1
        95.5%
        53%
        0.0
        jxe.111_R2
        87.2%
        54%
        0.0
        jxe.112_R1
        95.3%
        53%
        0.0
        jxe.112_R2
        90.3%
        54%
        0.0
        jxe.113_R1
        97.3%
        52%
        0.0
        jxe.113_R2
        91.0%
        54%
        0.0
        jxe.114_R1
        97.5%
        52%
        0.0
        jxe.114_R2
        92.2%
        54%
        0.0
        jxe.115_R1
        96.6%
        53%
        0.0
        jxe.115_R2
        87.6%
        54%
        0.0
        jxe.116_R1
        96.9%
        54%
        0.1
        jxe.116_R2
        90.9%
        55%
        0.1
        jxe.117_R1
        96.0%
        53%
        0.0
        jxe.117_R2
        89.5%
        54%
        0.0
        jxe.118_R1
        97.1%
        54%
        0.1
        jxe.118_R2
        91.3%
        55%
        0.1
        jxe.119_R1
        96.6%
        53%
        0.1
        jxe.119_R2
        90.2%
        54%
        0.1
        jxe.120_R1
        96.4%
        54%
        0.1
        jxe.120_R2
        89.7%
        54%
        0.1
        jxe.121_R1
        97.2%
        53%
        0.0
        jxe.121_R2
        89.2%
        54%
        0.0
        jxe.122_R1
        95.6%
        54%
        0.0
        jxe.122_R2
        88.3%
        54%
        0.0
        jxe.123_R1
        95.3%
        53%
        0.0
        jxe.123_R2
        85.8%
        54%
        0.0
        jxe.124_R1
        97.2%
        54%
        0.2
        jxe.124_R2
        93.0%
        55%
        0.2
        jxe.125_R1
        97.3%
        53%
        0.0
        jxe.125_R2
        90.1%
        54%
        0.0
        jxe.126_R1
        96.9%
        54%
        0.1
        jxe.126_R2
        90.4%
        55%
        0.1
        jxe.127_R1
        96.9%
        53%
        0.1
        jxe.127_R2
        86.2%
        55%
        0.1
        jxe.128_R1
        96.4%
        53%
        0.1
        jxe.128_R2
        89.6%
        54%
        0.1
        jxe.129_R1
        96.3%
        53%
        0.0
        jxe.129_R2
        90.1%
        54%
        0.0
        jxe.130_R1
        96.8%
        52%
        0.0
        jxe.130_R2
        90.7%
        54%
        0.0
        jxe.131_R1
        96.2%
        52%
        0.0
        jxe.131_R2
        89.3%
        54%
        0.0
        jxe.132_R1
        97.1%
        53%
        0.0
        jxe.132_R2
        89.6%
        54%
        0.0
        jxe.133_R1
        97.0%
        53%
        0.1
        jxe.133_R2
        90.1%
        54%
        0.1
        jxe.134_R1
        96.7%
        53%
        0.1
        jxe.134_R2
        90.2%
        54%
        0.1
        jxe.135_R1
        96.6%
        53%
        0.0
        jxe.135_R2
        87.3%
        55%
        0.0
        jxe.136_R1
        97.6%
        53%
        0.2
        jxe.136_R2
        93.9%
        54%
        0.2
        jxe.137_R1
        96.5%
        54%
        0.0
        jxe.137_R2
        89.9%
        55%
        0.0
        jxe.138_R1
        96.8%
        53%
        0.1
        jxe.138_R2
        91.4%
        54%
        0.1
        jxe.139_R1
        96.8%
        53%
        0.1
        jxe.139_R2
        86.9%
        54%
        0.1
        jxe.140_R1
        97.1%
        53%
        0.1
        jxe.140_R2
        90.7%
        54%
        0.1
        jxe.141_R1
        96.1%
        52%
        0.0
        jxe.141_R2
        88.1%
        54%
        0.0
        jxe.142_R1
        96.7%
        54%
        0.1
        jxe.142_R2
        88.7%
        54%
        0.1
        jxe.143_R1
        96.1%
        53%
        0.1
        jxe.143_R2
        87.8%
        54%
        0.1
        jxe.144_R1
        95.6%
        54%
        0.0
        jxe.144_R2
        87.2%
        54%
        0.0
        jxe.145_R1
        97.3%
        53%
        0.1
        jxe.145_R2
        89.1%
        53%
        0.1
        jxe.146_R1
        96.0%
        53%
        0.0
        jxe.146_R2
        87.1%
        54%
        0.0
        jxe.147_R1
        96.1%
        52%
        0.0
        jxe.147_R2
        86.0%
        54%
        0.0
        jxe.148_R1
        97.7%
        54%
        0.1
        jxe.148_R2
        93.3%
        55%
        0.1
        jxe.149_R1
        95.9%
        52%
        0.0
        jxe.149_R2
        87.2%
        54%
        0.0
        jxe.150_R1
        96.7%
        53%
        0.1
        jxe.150_R2
        89.9%
        54%
        0.1
        jxe.151_R1
        95.9%
        53%
        0.0
        jxe.151_R2
        84.0%
        55%
        0.0
        jxe.152_R1
        96.7%
        53%
        0.1
        jxe.152_R2
        89.2%
        54%
        0.1
        jxe.153_R1
        95.7%
        54%
        0.0
        jxe.153_R2
        87.1%
        55%
        0.0
        jxe.154_R1
        95.9%
        53%
        0.0
        jxe.154_R2
        87.6%
        54%
        0.0
        jxe.155_R1
        90.5%
        53%
        0.0
        jxe.155_R2
        76.5%
        54%
        0.0
        jxe.156_R1
        92.3%
        54%
        0.0
        jxe.156_R2
        81.0%
        54%
        0.0
        jxe.157_R1
        96.9%
        53%
        0.1
        jxe.157_R2
        86.8%
        54%
        0.1
        jxe.158_R1
        96.1%
        53%
        0.0
        jxe.158_R2
        87.1%
        54%
        0.0
        jxe.159_R1
        97.0%
        53%
        0.1
        jxe.159_R2
        86.8%
        54%
        0.1
        jxe.160_R1
        96.3%
        54%
        0.0
        jxe.160_R2
        89.6%
        55%
        0.0
        jxe.161_R1
        95.5%
        52%
        0.0
        jxe.161_R2
        86.4%
        54%
        0.0
        jxe.162_R1
        97.4%
        52%
        0.0
        jxe.162_R2
        90.6%
        54%
        0.0
        jxe.163_R1
        96.5%
        52%
        0.0
        jxe.163_R2
        84.6%
        54%
        0.0
        jxe.164_R1
        97.1%
        53%
        0.1
        jxe.164_R2
        89.2%
        54%
        0.1
        jxe.165_R1
        95.8%
        52%
        0.0
        jxe.165_R2
        89.5%
        54%
        0.0
        jxe.166_R1
        97.1%
        53%
        0.1
        jxe.166_R2
        90.1%
        54%
        0.1
        jxe.167_R1
        96.6%
        53%
        0.1
        jxe.167_R2
        90.2%
        54%
        0.1
        jxe.168_R1
        96.8%
        53%
        0.1
        jxe.168_R2
        89.7%
        54%
        0.1
        jxe.169_R1
        97.0%
        52%
        0.0
        jxe.169_R2
        89.0%
        54%
        0.0
        jxe.170_R1
        96.1%
        53%
        0.1
        jxe.170_R2
        89.1%
        54%
        0.1
        jxe.171_R1
        96.3%
        53%
        0.0
        jxe.171_R2
        87.1%
        54%
        0.0
        jxe.172_R1
        97.0%
        53%
        0.1
        jxe.172_R2
        92.9%
        54%
        0.1
        jxe.173_R1
        97.2%
        54%
        0.1
        jxe.173_R2
        90.7%
        55%
        0.1
        jxe.174_R1
        97.2%
        53%
        0.1
        jxe.174_R2
        90.6%
        55%
        0.1
        jxe.175_R1
        96.2%
        52%
        0.0
        jxe.175_R2
        85.7%
        54%
        0.0
        jxe.176_R1
        96.4%
        53%
        0.0
        jxe.176_R2
        88.7%
        54%
        0.0
        jxe.177_R1
        97.7%
        53%
        0.1
        jxe.177_R2
        91.6%
        54%
        0.1
        jxe.178_R1
        97.6%
        54%
        0.1
        jxe.178_R2
        91.1%
        54%
        0.1
        jxe.179_R1
        96.1%
        53%
        0.0
        jxe.179_R2
        89.2%
        54%
        0.0
        jxe.180_R1
        96.4%
        54%
        0.0
        jxe.180_R2
        89.7%
        55%
        0.0
        jxe.181_R1
        96.5%
        52%
        0.0
        jxe.181_R2
        89.0%
        54%
        0.0
        jxe.182_R1
        95.8%
        53%
        0.0
        jxe.182_R2
        87.8%
        54%
        0.0
        jxe.183_R1
        96.4%
        54%
        0.1
        jxe.183_R2
        88.8%
        54%
        0.1
        jxe.184_R1
        97.2%
        54%
        0.1
        jxe.184_R2
        93.0%
        54%
        0.1
        jxe.185_R1
        96.6%
        54%
        0.0
        jxe.185_R2
        88.5%
        55%
        0.0
        jxe.186_R1
        97.3%
        54%
        0.1
        jxe.186_R2
        91.4%
        55%
        0.1
        jxe.187_R1
        95.8%
        53%
        0.0
        jxe.187_R2
        85.2%
        54%
        0.0
        jxe.188_R1
        96.6%
        53%
        0.1
        jxe.188_R2
        90.2%
        54%
        0.1
        jxe.189_R1
        96.2%
        53%
        0.0
        jxe.189_R2
        88.9%
        55%
        0.0
        jxe.190_R1
        97.2%
        54%
        0.1
        jxe.190_R2
        91.0%
        55%
        0.1
        jxe.191_R1
        96.9%
        53%
        0.1
        jxe.191_R2
        90.9%
        54%
        0.1
        jxe.192_R1
        96.6%
        54%
        0.1
        jxe.192_R2
        90.6%
        54%
        0.1
        jxe.193_R1
        97.5%
        53%
        0.1
        jxe.193_R2
        90.4%
        54%
        0.1
        jxe.194_R1
        97.1%
        53%
        0.0
        jxe.194_R2
        90.9%
        54%
        0.0
        jxe.195_R1
        96.0%
        53%
        0.0
        jxe.195_R2
        87.8%
        54%
        0.0
        jxe.196_R1
        97.3%
        54%
        0.1
        jxe.196_R2
        93.6%
        55%
        0.1
        jxe.197_R1
        95.5%
        53%
        0.0
        jxe.197_R2
        88.0%
        54%
        0.0
        jxe.198_R1
        96.9%
        54%
        0.1
        jxe.198_R2
        91.5%
        54%
        0.1
        jxe.199_R1
        95.7%
        53%
        0.0
        jxe.199_R2
        84.9%
        54%
        0.0
        jxe.200_R1
        96.8%
        54%
        0.1
        jxe.200_R2
        90.2%
        54%
        0.1
        jxe.201_R1
        96.4%
        54%
        0.0
        jxe.201_R2
        88.8%
        56%
        0.0
        jxe.202_R1
        96.9%
        53%
        0.1
        jxe.202_R2
        90.1%
        54%
        0.1
        jxe.203_R1
        96.2%
        53%
        0.0
        jxe.203_R2
        88.0%
        55%
        0.0
        jxe.204_R1
        97.0%
        54%
        0.1
        jxe.204_R2
        91.3%
        54%
        0.1
        jxe.205_R1
        96.9%
        53%
        0.1
        jxe.205_R2
        88.2%
        54%
        0.1
        jxe.206_R1
        97.0%
        54%
        0.1
        jxe.206_R2
        90.5%
        54%
        0.1
        jxe.207_R1
        96.0%
        53%
        0.0
        jxe.207_R2
        86.6%
        54%
        0.0
        jxe.208_R1
        96.8%
        53%
        0.0
        jxe.208_R2
        92.4%
        54%
        0.0
        jxe.209_R1
        97.0%
        53%
        0.0
        jxe.209_R2
        90.5%
        54%
        0.0
        jxe.210_R1
        97.1%
        53%
        0.0
        jxe.210_R2
        91.7%
        54%
        0.0
        jxe.211_R1
        96.5%
        52%
        0.0
        jxe.211_R2
        87.4%
        54%
        0.0
        jxe.212_R1
        96.5%
        52%
        0.0
        jxe.212_R2
        89.8%
        54%
        0.0
        jxe.213_R1
        96.7%
        54%
        0.1
        jxe.213_R2
        90.9%
        54%
        0.1
        jxe.214_R1
        96.8%
        53%
        0.1
        jxe.214_R2
        89.5%
        55%
        0.1
        jxe.215_R1
        96.6%
        53%
        0.1
        jxe.215_R2
        88.9%
        54%
        0.1
        jxe.216_R1
        96.7%
        53%
        0.1
        jxe.216_R2
        89.3%
        55%
        0.1
        jxe.217_R1
        97.3%
        54%
        0.1
        jxe.217_R2
        88.7%
        55%
        0.1
        jxe.218_R1
        96.2%
        53%
        0.0
        jxe.218_R2
        88.4%
        54%
        0.0
        jxe.219_R1
        97.1%
        53%
        0.1
        jxe.219_R2
        89.6%
        54%
        0.1
        jxe.220_R1
        97.0%
        53%
        0.1
        jxe.220_R2
        92.3%
        54%
        0.1
        jxe.221_R1
        97.4%
        54%
        0.1
        jxe.221_R2
        90.4%
        55%
        0.1
        jxe.222_R1
        97.1%
        54%
        0.0
        jxe.222_R2
        90.0%
        55%
        0.0
        jxe.223_R1
        96.7%
        53%
        0.1
        jxe.223_R2
        86.5%
        55%
        0.1
        jxe.224_R1
        96.3%
        54%
        0.1
        jxe.224_R2
        88.9%
        55%
        0.1

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        No samples found with any adapter contamination > 0.1%

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        loading..

        MultiQC v1.10.1 - Written by Phil Ewels, available on GitHub.

        This report uses HighCharts, jQuery, jQuery UI, Bootstrap, FileSaver.js and clipboard.js.